Contacts of the helix formed by residues 69 - 83 (chain A) in PDB entry 1BSG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with CYS 69 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A PRO* 4.2 17.2 - - - +
68A MET* 1.3 84.5 - - - +
70A SER* 1.3 60.6 + - - +
71A VAL 3.1 4.3 + - - -
72A PHE* 3.0 25.4 + - - -
162A LEU* 5.6 0.2 - - - +
169A LEU* 3.9 15.6 + - - +
170A ASN* 3.5 30.7 - - - +
179A ASP* 4.5 1.8 + - - +
236A GLY* 4.2 2.2 - - - -
237A ALA 4.0 15.7 - - - +
238A GLY* 3.9 11.4 - - - -
243A THR* 3.6 27.8 - - - -
245A ASN* 4.2 2.0 - - - +
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Residues in contact with SER 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A CYS* 1.3 75.7 - - - +
71A VAL* 1.3 59.6 + - - +
72A PHE* 2.9 14.6 + - - +
73A LYS* 2.8 38.6 + - - +
130A SER* 3.4 17.7 + - - -
132A ASN* 4.4 1.4 + - - -
166A GLU* 3.9 4.2 + - - -
170A ASN* 4.2 4.2 + - - -
234A LYS* 3.3 14.3 - - - -
235A THR 3.4 17.9 - - - -
236A GLY* 3.8 6.1 - - - -
237A ALA 5.0 3.6 + - - -
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A MET* 3.4 25.8 - - + +
69A CYS 3.1 1.0 + - - -
70A SER* 1.3 76.7 - - - +
72A PHE* 1.3 60.2 + - - +
73A LYS 3.4 0.7 + - - -
74A THR 3.7 2.4 + - - -
75A LEU* 4.3 1.2 - - - +
181A THR* 5.3 1.6 - - + -
186A ILE* 3.7 31.0 - - + -
190A TYR* 2.7 39.0 + - + +
234A LYS* 3.9 22.4 - - - +
235A THR 3.7 5.7 + - - -
236A GLY* 4.3 0.2 - - - -
245A ASN* 3.8 24.7 - - + +
247A ALA* 4.5 10.1 - - + -
264A LEU* 4.9 4.5 - - + -
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Residues in contact with PHE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A MET* 3.8 29.6 - - + +
69A CYS 3.0 26.2 + - - +
70A SER* 2.9 2.5 - - - -
71A VAL* 1.3 75.5 - - - +
73A LYS* 1.3 79.6 + - + +
74A THR 3.1 2.7 - - - -
75A LEU* 2.8 30.1 + - + +
76A SER* 3.1 32.0 + - - -
135A ALA* 3.9 13.0 - - + -
139A LEU* 4.4 10.5 - - + -
148A VAL* 5.1 2.5 - - + -
162A LEU* 3.8 27.8 - - + -
166A GLU* 3.3 27.8 - - + -
169A LEU* 3.5 24.2 - - + -
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Residues in contact with LYS 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A SER* 2.8 41.5 + - - +
72A PHE* 1.3 90.6 - - + +
74A THR* 1.3 60.5 + - - +
76A SER* 3.1 18.0 + - - -
77A SER* 3.1 18.2 + - - -
126A SER* 3.2 32.5 - - - +
127A ILE* 4.2 3.0 - - - +
130A SER* 3.0 20.8 + - - +
131A ASP 4.1 3.1 - - - -
132A ASN* 2.9 25.0 + - - +
135A ALA* 3.8 25.1 - - + -
166A GLU* 3.2 18.4 + - - -
234A LYS* 3.8 4.5 - - - -
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Residues in contact with THR 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A VAL 3.7 0.4 + - - -
72A PHE 3.1 0.6 - - - -
73A LYS* 1.3 78.7 - - - +
75A LEU* 1.3 57.9 + - - +
77A SER* 3.9 1.9 - - - -
78A ALA* 3.0 27.3 + - - +
127A ILE* 4.2 10.3 - - + +
190A TYR* 2.7 45.5 + - + -
193A LEU* 4.4 8.1 - - + -
194A VAL* 6.0 0.7 - - + -
207A LEU* 4.0 24.4 - - + +
211A LEU* 3.9 18.1 - - + +
234A LYS* 3.3 19.2 - - - +
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A MET* 4.3 2.7 - - - -
71A VAL 4.3 3.4 - - - +
72A PHE* 2.8 26.0 + - + +
74A THR* 1.3 76.2 - - - +
76A SER* 1.3 58.4 + - - +
78A ALA* 3.4 5.1 + - - +
79A ALA* 3.0 29.1 + - - +
148A VAL* 4.0 18.2 - - + -
151A PHE* 3.8 8.8 - - + -
152A VAL* 3.8 23.1 - - + -
160A THR* 3.9 20.2 - - + -
186A ILE* 4.1 9.9 - - + -
189A THR* 3.7 26.9 - - + -
190A TYR* 4.1 14.8 - - + -
193A LEU* 4.0 14.1 - - + -
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Residues in contact with SER 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 3.1 15.0 + - - -
73A LYS* 3.1 26.3 + - - +
75A LEU* 1.3 75.0 - - - +
77A SER* 1.3 63.1 + - - +
79A ALA* 3.2 4.9 + - - +
80A VAL* 3.2 25.6 + - - +
126A SER* 5.3 1.9 - - - -
135A ALA* 4.9 4.6 - - - +
138A MET* 5.0 9.7 - - - +
139A LEU* 4.3 11.2 - - - -
142A LEU* 3.7 21.0 - - - +
148A VAL* 4.2 16.5 - - - +
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Residues in contact with SER 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LYS 3.1 19.1 + - - -
74A THR 3.9 3.1 - - - -
76A SER* 1.3 78.1 + - - +
78A ALA* 1.3 62.6 + - - +
80A VAL* 3.2 13.3 + - - +
81A LEU* 3.2 18.0 + - - +
123A CYS* 2.9 49.3 + - - -
126A SER* 3.9 7.3 + - - -
127A ILE* 4.0 12.8 - - - +
138A MET* 5.4 2.2 - - - +
207A LEU* 4.5 0.7 - - - -
210A TRP* 4.2 5.6 - - - -
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Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A THR 3.0 19.7 + - - +
75A LEU 3.7 4.5 - - - +
76A SER 3.3 0.2 - - - -
77A SER* 1.3 77.5 - - - +
79A ALA* 1.3 58.1 + - - +
81A LEU* 3.3 13.8 + - - +
82A ARG* 3.0 30.0 + - - +
151A PHE* 3.9 15.7 - - + -
193A LEU* 3.9 22.9 - - + -
199A LEU* 3.8 5.7 - - + +
207A LEU* 4.2 10.3 - - + +
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU 3.0 13.7 + - - +
76A SER* 3.2 9.8 + - - +
78A ALA* 1.3 75.2 - - - +
80A VAL* 1.3 59.9 + - - +
83A ASP* 2.9 37.0 + - - +
84A LEU 3.8 0.2 + - - -
142A LEU* 3.8 22.0 - - + +
147A ALA 5.2 2.7 - - - +
148A VAL* 5.6 2.2 - - + -
151A PHE* 3.9 34.0 - - + -
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A SER 3.2 14.3 + - - +
77A SER 3.2 6.7 + - - +
79A ALA* 1.3 73.7 - - - +
81A LEU* 1.3 60.2 + - - +
84A LEU* 2.9 38.0 + - + +
85A ASP* 3.0 9.8 + - - +
90A PHE* 4.1 16.8 - - + -
91A LEU* 4.3 7.9 - - + -
119A VAL* 3.8 27.6 - - + -
123A CYS* 3.8 17.3 - - - -
138A MET* 4.1 17.9 - - + +
142A LEU* 4.1 18.6 - - + -
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A SER 3.2 12.9 + - - +
78A ALA* 3.4 12.3 - - - +
80A VAL* 1.3 82.8 - - + +
82A ARG* 1.3 61.3 + - - +
85A ASP* 3.3 22.8 - - + +
91A LEU* 3.9 33.2 - - + -
123A CYS* 5.6 0.7 - - - -
199A LEU* 4.5 3.4 - - + -
203A ASP* 3.4 52.6 - - + +
206A LEU* 4.1 9.0 - - + -
207A LEU* 4.1 12.8 - - + +
210A TRP* 3.9 33.0 - - + -
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Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ALA 3.0 15.6 + - - +
81A LEU* 1.3 77.9 - - - +
83A ASP* 1.3 93.0 + - - +
85A ASP 4.3 5.4 - - - +
151A PHE* 3.4 24.7 - - + +
154A SER* 2.9 35.9 + - - -
155A LEU* 3.6 20.4 - - - +
198A ALA 3.7 21.0 + - - +
199A LEU* 3.7 14.3 - - + +
200A ASN 6.2 0.2 - - - +
203A ASP* 4.4 4.3 - - - -
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Residues in contact with ASP 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ALA* 2.9 20.4 + - + +
82A ARG* 1.3 119.2 + - - +
84A LEU* 1.3 70.4 + - + +
85A ASP 5.0 0.7 - - - -
142A LEU* 5.6 2.0 - - + -
150A ARG* 5.5 6.2 + - - +
151A PHE* 3.9 11.3 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il